| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-05-09 11:41:11 -0400 (Thu, 09 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4748 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4484 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4514 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" | 4480 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1430/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| nipalsMCIA 1.2.0 (landing page) Maximilian Mattessich
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the nipalsMCIA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/nipalsMCIA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: nipalsMCIA |
| Version: 1.2.0 |
| Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings nipalsMCIA_1.2.0.tar.gz |
| StartedAt: 2024-05-09 10:05:07 -0000 (Thu, 09 May 2024) |
| EndedAt: 2024-05-09 10:13:06 -0000 (Thu, 09 May 2024) |
| EllapsedTime: 478.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: nipalsMCIA.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:nipalsMCIA.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings nipalsMCIA_1.2.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/nipalsMCIA.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nipalsMCIA/DESCRIPTION’ ... OK
* this is package ‘nipalsMCIA’ version ‘1.2.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘nipalsMCIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
nipals_multiblock 18.602 0.088 18.733
block_weights_heatmap 17.020 0.451 17.509
get_colors 15.378 0.119 15.533
get_metadata_colors 15.275 0.104 15.413
vis_load_plot 14.996 0.052 15.081
vis_load_ord 14.682 0.024 14.739
global_scores_eigenvalues_plot 13.746 0.036 13.814
ord_loadings 13.319 0.043 13.393
projection_plot 12.856 0.024 12.912
nmb_get_gs 10.198 0.076 10.298
nmb_get_eigs 10.208 0.000 10.230
nmb_get_bs 9.797 0.048 9.867
nmb_get_metadata 9.718 0.008 9.749
nmb_get_bs_weights 9.119 0.000 9.140
nmb_get_gl 9.114 0.004 9.139
nmb_get_bl 8.977 0.028 9.026
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
nipalsMCIA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL nipalsMCIA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’ * installing *source* package ‘nipalsMCIA’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (nipalsMCIA)
nipalsMCIA.Rcheck/tests/testthat.Rout
R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
>
> library(nipalsMCIA)
> library(testthat)
>
> test_check("nipalsMCIA")
Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Computing order 3 scores
Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Running GSEA for Factor 1
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Performing column-level pre-processing...
Column pre-processing completed.
Performing block-level preprocessing...
Block pre-processing completed.
Computing order 1 scores
Computing order 2 scores
Computing order 3 scores
Computing order 4 scores
Performing pre-processing on data
Pre-processing completed
color_col option not recognized, defaulting to black/white plotting.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> proc.time()
user system elapsed
46.964 2.410 53.408
nipalsMCIA.Rcheck/nipalsMCIA-Ex.timings
| name | user | system | elapsed | |
| block_preproc | 0.001 | 0.000 | 0.001 | |
| block_weights_heatmap | 17.020 | 0.451 | 17.509 | |
| cc_preproc | 0.001 | 0.000 | 0.000 | |
| col_preproc | 0 | 0 | 0 | |
| deflate_block_bl | 0.000 | 0.000 | 0.001 | |
| deflate_block_gs | 0.000 | 0.001 | 0.000 | |
| extract_from_mae | 0.866 | 0.078 | 0.946 | |
| get_colors | 15.378 | 0.119 | 15.533 | |
| get_metadata_colors | 15.275 | 0.104 | 15.413 | |
| get_tv | 0.329 | 0.000 | 0.329 | |
| global_scores_eigenvalues_plot | 13.746 | 0.036 | 13.814 | |
| nipals_iter | 0.37 | 0.00 | 0.37 | |
| nipals_multiblock | 18.602 | 0.088 | 18.733 | |
| nmb_get_bl | 8.977 | 0.028 | 9.026 | |
| nmb_get_bs | 9.797 | 0.048 | 9.867 | |
| nmb_get_bs_weights | 9.119 | 0.000 | 9.140 | |
| nmb_get_eigs | 10.208 | 0.000 | 10.230 | |
| nmb_get_gl | 9.114 | 0.004 | 9.139 | |
| nmb_get_gs | 10.198 | 0.076 | 10.298 | |
| nmb_get_metadata | 9.718 | 0.008 | 9.749 | |
| ord_loadings | 13.319 | 0.043 | 13.393 | |
| predict_gs | 1.715 | 0.024 | 1.743 | |
| projection_plot | 12.856 | 0.024 | 12.912 | |
| simple_mae | 0.482 | 0.000 | 0.483 | |
| vis_load_ord | 14.682 | 0.024 | 14.739 | |
| vis_load_plot | 14.996 | 0.052 | 15.081 | |